1-182570983-C-T

Position:

• chr1-182570983-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.11 in 152,142 control chromosomes in the GnomAD database, including 990 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (990 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16698 AN: 152024 Hom.: 990 Cov.: 32

Gnomad AFR AF: 0.0989

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0873

Gnomad ASJ AF: 0.0821

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.0199

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.102

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.110 AC: 16705 AN: 152142 Hom.: 990 Cov.: 32 AF XY: 0.108 AC XY: 8048 AN XY: 74376

Gnomad4 AFR AF: 0.0987

Gnomad4 AMR AF: 0.0871

Gnomad4 ASJ AF: 0.0821

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0205

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.101

Alfa AF: 0.123 Hom.: 156

Bravo AF: 0.107

Asia WGS AF: 0.0180 AC: 65 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.82

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12729828; hg19: chr1-182540118;